Fig. 3

Pan-cancer relative enrichment of mutations in T cell-inflamed and non-inflamed tumors from all protein-coding genes on the genome. a Twenty-nine genes carrying NSSMs more frequently in non-T cell-inflamed relative to T cell-inflamed tumors at FDR-adjusted P < 0.10. b Three genes carrying NSSMs more frequent in T cell-inflamed relative to non-T cell-inflamed tumors at FDR-adjusted P < 0.10. The full list of genes with statistical metrics across all tumors is provided in Additional file 1: Table S6 and Additional file 1: Table S7. c Representative examples showing the protein-domain-specific enrichment of non-T cell-inflamed mutations in IDH1, CTNNB1, CIC, and NRAS pan-cancer wide. Individual amino acid changes are shown on the x-axis when space permits. The predicted mutation effects (loss of function (LOF), gain of function (GOF), etc.) of the 29 genes shown in a and three genes shown in b are provided in Additional file 1: Table S8 with summary statistics in Additional file 1: Table S9. For a and b, genes mutated in at least 0.5% of the samples pooled from all tumor types were included in statistical testing. Logistic regression with TMB as a covariate was used in a and b, with BH-FDR correction for multiple comparisons